Table 1.

Proportion of Pairwise Homologies Retained after Treatment in Core Regions.

Data Set	Divvying						Partial Filtering
	Reference MSA	Mafft-FFT-ns	Mafft-lin-si	Prank	Probcons	T-Coffee	Reference MSA	Mafft-FFT-ns	Mafft-lin-si	Prank	Probcons	T-Coffee
BBS11	0.22	0.23	0.23	0.24	0.23	0.23	0.18	0.19	0.18	0.19	0.18	0.18
BBS12	0.66	0.68	0.68	0.7	0.67	0.67	0.62	0.64	0.63	0.65	0.63	0.63
BBS20	0.81	0.82	0.82	0.84	0.82	0.82	0.78	0.79	0.79	0.81	0.79	0.79
BBS30	0.56	0.57	0.56	0.63	0.56	0.56	0.48	0.49	0.48	0.54	0.49	0.48
BBS50	0.5	0.52	0.51	0.58	0.51	0.51	0.41	0.43	0.41	0.48	0.42	0.41

Note.—Proportion of residue pairs after treating reference and inferred MSAs using divvier. The numbers represent fraction of pairwise homologies remaining following divvying and partial filtering.